Research Article: Ochrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains

Date Published: January 22, 2019

Publisher: Public Library of Science

Author(s): Dorota M. Krzyżanowska, Tomasz Maciąg, Adam Ossowicki, Magdalena Rajewska, Zbigniew Kaczyński, Małgorzata Czerwicka, Łukasz Rąbalski, Paulina Czaplewska, Sylwia Jafra, Axel Cloeckaert.

http://doi.org/10.1371/journal.pone.0210874

Abstract

Ochrobactrum spp. are ubiquitous bacteria attracting growing attention as important members of microbiomes of plants and nematodes and as a source of enzymes for biotechnology. Strain Ochrobactrum sp. A44T was isolated from the rhizosphere of a field-grown potato in Gelderland, the Netherlands. The strain can interfere with quorum sensing (QS) of Gram-negative bacteria through inactivation of N-acyl homoserine lactones (AHLs) and protect plant tissue against soft rot pathogens, the virulence of which is governed by QS. Phylogenetic analysis based on 16S rRNA gene alone and concatenation of 16S rRNA gene and MLSA genes (groEL and gyrB) revealed that the closest relatives of A44T are O. grignonense OgA9aT, O. thiophenivorans DSM 7216T, O. pseudogrignonense CCUG 30717T, O. pituitosum CCUG 50899T, and O. rhizosphaerae PR17T. Genomes of all six type strains were sequenced, significantly expanding the possibility of genome-based analyses in Ochrobactrum spp. Average nucleotide identity (ANIb) and genome-to-genome distance (GGDC) values for A44T and the related strains were below the single species thresholds (95% and 70%, respectively), with the highest scores obtained for O. pituitosum CCUG 50899T (87.31%; 35.6%), O. rhizosphaerae PR17T (86.80%; 34.3%), and O. grignonense OgA9aT (86.30%; 33.6%). Distinction of A44T from the related type strains was supported by chemotaxonomic and biochemical analyses. Comparative genomics revealed that the core genome for the newly sequenced strains comprises 2731 genes, constituting 50–66% of each individual genome. Through phenotype-to-genotype study, we found that the non-motile strain O. thiophenivorans DSM 7216T lacks a cluster of genes related to flagella formation. Moreover, we explored the genetic background of distinct urease activity among the strains. Here, we propose to establish a novel species Ochrobactrum quorumnocens, with A44T as the type strain (= LMG 30544T = PCM 2957T).

Partial Text

Ochrobactrum spp., together with the closely related Brucella, Agrobacterium, and Rhizobium genera, belong to the class of Alphaproteobacteria [1–3]. Although the genus is most often associated with O. anthropi [4] and O. intermedium [1], which cause opportunistic infections in humans, the bacteria from the Ochrobactrum spp. genus adapted to a variety of environmental niches and can be found in soil [5], wastewater [6], in association with plants [6,7], and animals [8,9]. The ability of Ochrobactrum spp. members to utilize xenobiotic compounds led to their exploration as potential bioremediation agents [10–13] or a source of enzymes for the biotech industry [14,15]. Ochrobactrum spp. are also of interest as plant beneficial bacteria [16,17]. The plant-derived strains, such as O. lupini LUP21T [7] and O. cytisi ESC1T [18], are able to nodulate roots to fix nitrogen, underlining their close association with the host plants. Currently, the Ochrobactrum genus comprises 18 species [19] (Fig 1A). However, scientific data concerning the majority of the strains is limited to information of taxonomic value.

Ochrobactrum spp. receive growing interest as members of plant and nematode microbiomes and as potent tools in biotechnology. In this study, on the basis of sequence-based and phenotypic analyses, we propose to establish the QS-interfering strain A44T as a type strain of a novel species: Ochrobactrum quorumnocens sp. nov. (Taxonumber TA00464). The strain possesses a multi-replicon genome, characteristic for this genus. Before this study, genomes of only 2 out of 18 Ochrobactrum spp. type strains were available. Obtaining draft genomes of 5 of A44T-related type strains significantly contributes to the application of golden standard, genome-based approaches in taxonomy of this genus, especially in the light of an increasing number of genome assemblies for new strains, provisionally classified as Ochrobactrum sp. To our knowledge, this is the first study in which comparative genome analyses was performed for members of different Ochrobactrum species. Moreover, phenotype-to-genotype approach revealed the genetic background of the lack of motility in O. thiophenivorans DSM 7217T and showed the diversity of urease cluster organization in the studied group of Ochrobactrum spp. strains.

 

Source:

http://doi.org/10.1371/journal.pone.0210874

 

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